So, I'm trying to use the HDOCK server for docking. The problem is when I run it from my mac, it gives me error saying "too much residues" but when my friend run it from windows OS, it runs and also shows result. FYI, the files that we're using are identical plus I also tried using the one from her OS, downloaded and ran, still same error. Attaching the screenshot of that error.
Any idea how to fix it? or what seems to be the problem?
Thanks in advance!
This could be caused by the line endings that differ between macOS and Windows. Generally a utility like dos2unix can help fix this. You could give the following a try in case you don't want to install that utility.
The "too much residues" error in HDOCK typically arises from subtle formatting issues in the PDB input file, such as encoding or invisible characters that differ between Mac and Windows despite identical content. Since line-ending fixes with sed did not resolve it, the problem may lie in byte-level variations introduced during file handling on your system.
To diagnose, compare the binary contents of the PDB files from both OSes using a hex editor or a binary diff tool—this should reveal any hidden discrepancies. You could also try uploading via a different browser (or incognito mode) or even command-line tools like curl to bypass potential Mac-specific upload quirks.
If those steps fail, I recommend emailing the HDOCK team directly with your files and screenshot for targeted help.
This could be caused by the line endings that differ between macOS and Windows. Generally a utility like
dos2unixcan help fix this. You could give the following a try in case you don't want to install that utility.Tried that but unfortunately, the problem still persists :( Thanks for your response though!